Interactive 3D Complements in Proteopedia

Articles in Proteopedia can be designed to complement publications in scientific journals. A link, within the publication, to an interactive 3D complement (I3DC) in Proteopedia can enable readers to rotate molecular scenes having the same initial orientation, color schemes, and labeling as figures in the publication. Links to the interactive 3D complement in Proteopedia can be placed in the text of the publication, and/or in the .doc file included on the journal website as supplementary materials. The I3DC article can be developed in advance of publication, yet hidden from viewing by visitors to Proteopedia until publication occurs (see Proteopedia:Workbench). Authors of the associated publications are able and encouraged to review the I3DC page before publication, and to interact with the Proteopedia editor at any time. I3DC are protected from editing by anyone.

Proteopedia is working with Journals to develop, in close collaboration with authors, interactive 3D complement articles in Proteopedia, thus rendering the structural data more comprehensible to a wider audience. In addition, Proteopedia welcomes author-initiated development of interactive 3D complement articles for individual publications in any journal.

For more details, please contact

Journals Adopting I3DC
The Journal of Biological Inorganic Chemistry seeks to promote this field internationally. This journal is primarily concerned with advances in the understanding of systems involving one or more metal ions set in a biological matrix--particularly, metalloproteins and metal-nucleic acid complexes--in order to understand biological function at the atomic level. Manuscripts describing high quality and original research concerned with metal ions or other inorganic species and having biological relevance are invited for submission to this journal. Mini-reviews, Reports, and Commentaries are also encouraged. Examples can be found in the list of I3DC articles for JBIC.

Author-Initiated I3DC
Proteopedia encourages authors of any scientific publication to develop an interactive 3D complement in Proteopedia. Members of the Proteopedia team stand ready to assist:. Here are some examples of author-initiated I3DC:


 * User:Janice C. Telfer/Group B SRCR domains provides interactive 3D complements linked into the discussion of the publication Scavenger receptor WC1 contributes to the γδ T cell response to Leptospira (2011).
 * Engineered mutants of HlyIIR provides interactive 3D complements for a publication in Proteins (2010).
 * The publication of 3btp in Proc. Natl. Acad. Sci. USA (2008) was accompanied by an I3DC.

I3DC vs. Supplementary Materials
Interactive 3D complements in Proteopedia have some functions in common with supplementary materials, but are distinguished because
 * 1) The journal does not hold a copyright to the the interactive 3D complement (I3DC).
 * 2) I3DC fall under the the same licenses as do all contributions to Proteopedia (for details, please see Proteopedia:Terms of Service).
 * 3) The I3DC is not housed on the journal's website.
 * 4) The I3DC is not frozen. It can be edited by the authors of the publication, subsequent to publication, should the authors wish to do so.

Protection From Editing
Unlike most articles in Proteopedia, I3DC are not open to editing by the general community of Proteopedia account holders.
 * For journals with formal I3DC adoption policies, the I3DC are placed within the Journal: namespace. This protects them.
 * Author-initiated I3DC should be placed within an author's User: space, which protects them (see Help:Protected Pages).